[gmx-users] REMD

[Dongsheng Zhang]

Dear David,

I believe it runs in two processors because I can get two log files. I
tried to use mpirun, the computer complains that command mpirun (or
mpi_run) not found.

Replica1.log stops at:
Rel. Constraint Deviation:  Max    between atoms     RMS

Then I search where those messages are from in the source code. I found
they are in  mdlib/clincs.c, as following:


    if (do_per_step(step,ir->nstlog) || (step < 0)) {
      fprintf(stdlog,"   Rel. Constraint Deviation:  Max    between
atoms     RMS\n");
      fprintf(stdlog,"       Before LINCS         %.6f %6d %6d   %.6f
\n",
	      p_max,lincsd->bla[2*p_imax]+1,lincsd->bla[2*p_imax+1]+1,p_rms);
      cconerr(&p_max,&p_rms,&p_imax,xprime,pbc_null,
	      lincsd->nc,lincsd->bla,lincsd->bllen);
      fprintf(stdlog,"        After LINCS         %.6f %6d %6d   %.6f\n
\n",
	      p_max,lincsd->bla[2*p_imax]+1,lincsd->bla[2*p_imax+1]+1,p_rms);
    }


I have a question about these codes, why does the output process stop in
the middle? (Disk space is very large, not full)


thank you for your help!


Dongsheng


On Thu, 2006-04-13 at 16:13 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Dear David,
> > 
> > I forgot one more information. The computer administrator told me I did
> > not need to use mpirun. As I told you in the previous email, I have done
> > tests for parallel computing. It worked fine.
> > 
> try it with mpirun anyway.
> 
> I suspect you are just running a single process which crashes as soon as 
> it needs to do REMD communication.
> 
> 
> > Dongsheng
> > 
> > On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote:
> >> Dongsheng Zhang wrote:
> >>> dear Mark,
> >>>
> >>> Thank you very much for your prompt reply.  I try to use parallel
> >>> computing. It works fine.
> >>> for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle     
> >>>              to  get replica0.tpr
> >>>              then, mdrun_mpi -np 2 -s replica0.tpr
> >>>
> >> please give EXACT command line and do use mpirun
> >>
> >>
> >>> The error message mentioned in the previous email looks very strange to
> >>> me. MPI works fine, and individual tpr runs fine. The error message
> >>> comes out before replica exchange. replica0 stops at step 500, replica1
> >>> stops at step 400, even the output informatio can't be complted. The
> >>> last lines in replica1.log is
> >>>
> >>>         Step           Time         Lambda
> >>>             400        0.80000        0.00000
> >>>
> >>>    Rel. Constraint Deviation:  Max    between atoms     RMS
> >>>
> >>>
> >>> I hope these further information can help you to figure out what's the
> >>> problem.
> >>>
> >>> Best Wishes!
> >>>
> >>> Dongsheng
> >>>
> >>>
> >>> On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote: 
> >>>>> Dear gmx users:
> >>>>>
> >>>>> I am trying to run REMD with two replicas (for testing). I used
> >>>>> grompp -f -c -p -o replica0 to get replica0.tpr
> >>>>> grompp -f -c -p -o replica1 to get replica1.tpr
> >>>>>
> >>>>> then used
> >>>>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> >>>>> -v -N 2
> >>>>> to run it.
> >>>> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
> >>>> looks fine to me.
> >>>>
> >>>>> I got an error message "Segmentation fault" from my script output, but
> >>>>> no error message in both log files. When I tried to run individual tpr
> >>>>> file, it worked fine.
> >>>>>
> >>>>> Could someone can comment why I got "Segmentation fault"? Thank you for
> >>>>> your help!
> >>>> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
> >>>> ..." to make it work - the segfault might be a gromacs-MPI interaction
> >>>> problem. If you can run an MPI process from the command line you may get
> >>>> more helpful feedback.
> >>>>
> >>>> Mark
> >>>>
> >>>> _______________________________________________
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> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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